- Likelihood - package Likelihood
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Provides classes for calculating the likelihood of a tree given a model and
an alignment.
- Likelihood - Class in Likelihood
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Represents the simplest possible likelihood result, i.e.
- Likelihood(double, Parameters) - Constructor for class Likelihood.Likelihood
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Creates a simple likelihood result
- likelihood(Alignment) - Method in interface ModelTest.Adapter
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Return the likelihood of the adapter given the distinct alignment
- likelihood(Alignment) - Method in class ModelTest.EmpiricalAdapter
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- likelihood(Alignment) - Method in class ModelTest.EqualAdapter
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- likelihood(Alignment) - Method in class ModelTest.IdentityAdapter
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- limitToTaxa(Collection<String>) - Method in class Alignments.Alignment
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Returns a new Alignment which is the same as this one except it is limited
to certain taxa
- limitToTaxa(Collection<String>) - Method in class Alignments.Site
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Returns a new Site which is the same as this one except it is limited
to certain taxa
- ln() - Method in interface Maths.Real
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Returns the natural logarithm of this Real
- ln() - Method in class Maths.SmallDouble
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- ln() - Method in class Maths.StandardDouble
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- ln1m() - Method in interface Maths.Real
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Returns the natural logithm of one minus the value of this Real
- ln1m() - Method in class Maths.SmallDouble
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- ln1m() - Method in class Maths.StandardDouble
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- lower() - Method in class Utils.Range
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Gets the lower value
- LUDecomposition - Class in Maths
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LU Decomposition.
- LUDecomposition(SquareMatrix) - Constructor for class Maths.LUDecomposition
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LU Decomposition